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- PDB-6sup: Crystal Structure of TcdB2-TccC3-Cdc42 -

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Basic information

Entry
Database: PDB / ID: 6sup
TitleCrystal Structure of TcdB2-TccC3-Cdc42
ComponentsTcdB2,TccC3,Cell division control protein 42 homolog
KeywordsTOXIN / Toxins / Tc Toxins
Function / homology
Function and homology information


GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination ...GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / GTP-dependent protein binding / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / nuclear migration / small GTPase-mediated signal transduction / Myogenesis / positive regulation of cytokinesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of substrate adhesion-dependent cell spreading / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / actin filament organization / EGFR downregulation / small monomeric GTPase / integrin-mediated signaling pathway / MAPK6/MAPK4 signaling / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / filopodium / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis / G beta:gamma signalling through CDC42 / mitotic spindle / ubiquitin protein ligase activity / apical part of cell / intracellular protein localization / cell-cell junction / Factors involved in megakaryocyte development and platelet production / G protein activity / actin cytoskeleton organization / positive regulation of cell growth / midbody / neuron projection / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynapse / positive regulation of MAPK cascade / positive regulation of cell migration / Golgi membrane
Similarity search - Function
Shell / RHS repeat-associated core / RHS repeat-associated core / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat ...Shell / RHS repeat-associated core / RHS repeat-associated core / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / Cdc42 / Rhs repeat-associated core / : / Small GTPase Rho / Small GTPase Rho domain profile. / Integrin alpha, N-terminal / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Cell division control protein 42 homolog / TccC3 / TcdB2
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRoderer, D. / Schubert, E. / Sitsel, O. / Raunser, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council615984 Germany
CitationJournal: Nat Commun / Year: 2019
Title: Towards the application of Tc toxins as a universal protein translocation system.
Authors: Daniel Roderer / Evelyn Schubert / Oleg Sitsel / Stefan Raunser /
Abstract: Tc toxins are bacterial protein complexes that inject cytotoxic enzymes into target cells using a syringe-like mechanism. Tc toxins are composed of a membrane translocator and a cocoon that ...Tc toxins are bacterial protein complexes that inject cytotoxic enzymes into target cells using a syringe-like mechanism. Tc toxins are composed of a membrane translocator and a cocoon that encapsulates a toxic enzyme. The toxic enzyme varies between Tc toxins from different species and is not conserved. Here, we investigate whether the toxic enzyme can be replaced by other small proteins of different origin and properties, namely Cdc42, herpes simplex virus ICP47, Arabidopsis thaliana iLOV, Escherichia coli DHFR, Ras-binding domain of CRAF kinase, and TEV protease. Using a combination of electron microscopy, X-ray crystallography and in vitro translocation assays, we demonstrate that it is possible to turn Tc toxins into customizable molecular syringes for delivering proteins of interest across membranes. We also infer the guidelines that protein cargos must obey in terms of size, charge, and fold in order to apply Tc toxins as a universal protein translocation system.
History
DepositionSep 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TcdB2,TccC3,Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,9034
Polymers240,8311
Non-polymers733
Water23,0411279
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-25 kcal/mol
Surface area86710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.350, 156.550, 179.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TcdB2,TccC3,Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 240830.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria), (gene. exp.) Homo sapiens (human)
Gene: tcdB2, TccC3, CDC42 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8GF99, UniProt: Q8GF97, UniProt: P60953, small monomeric GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1279 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium chloride, 0.1 M magnesium chloride, 0.1 M tri-sodium citrate pH 5.5, 12 % PEG 4000 Seeding: 0.1 M magnesium chloride, 0.1 M tri-sodium acetate pH 4.6, 12 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97958 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2→48.17 Å / Num. obs: 182401 / % possible obs: 99.9 % / Redundancy: 22 % / CC1/2: 0.998 / Net I/σ(I): 13.81
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1.46 / Num. unique obs: 18014 / CC1/2: 0.688

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSVERSION Mar 15, 2019 BUILT=20190315data reduction
XSCALEVERSION Mar 15, 2019 BUILT=20190315data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O9X

4o9x


Resolution: 2→48.17 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.32 --
Rwork0.287 --
obs-182143 99.5 %
Refinement stepCycle: LAST / Resolution: 2→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17002 0 3 1282 18287

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